[gmx-users] Osmotic pressure

[Mark Abraham]

Hi,

Also you can choose coupling algorithms that are known to sample correct
ensembles...

Mark

On Fri, 15 Apr 2016 11:50 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/15/16 5:20 AM, gozde ergin wrote:
> > Dear all,
> >
> > I simulate the NaCl solution to estimate the osmotic pressure. My salt
> concentrations are 3,4 and 5M. I apply flat-bottom restraint to the
> molecules.
> > I use CHARMM36 ff with NBFIX correction.
> >
> > After the simulation I extract the z-coordinates of restraint ions and
> use the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic
> pressure.
> > Actually I try to get the similar results as Lou&Roux 2010 study.
> >
> > However my osmotic pressure results are on the line of ideal solution
> osmotic pressure as shown equation in below;
> >
> > P = cRT (Van’t Hoff equation)
> >
> > but not the similar result with experiments.
> >
>
> What values do you actually get?  How do they compare with the values from
> the
> Roux paper?  Are you remembering to divide by 2*area in your calculation
> (since
> you have two walls)?
>
> > Is there anyone here that get the same trend as me for osmotic pressure
> calculation? Or is there something that I miss?
> >
> >
> > Here is my .mdp file;
> >
> > define                   = -DPOSRES
> > integrator               = md
> > dt                       = 0.002
> > nsteps                   = 2500000   ;
> > ; Output control
> > nstxout                  = 2000
> > nstvout                  = 2000
> > nstlog                   = 2000
> > nstenergy                = 2000
> > ; Bond parameters
> > continuation         = no        ;
> > constraint_algorithm = shake     ; h
> > constraints          = all-bonds ; a
> > shake_tol            = 0.0001
> > ; Neighborsearching
> > ns_type     = grid              ;
> > nstlist     = 5                 ;
> > rlist       = 1.1               ;
> > rcoulomb    = 1.1               ;
> > rvdw        = 1.1               ;
>
> These nonbonded settings are wrong.  The values for CHARMM36 are well
> established and you should not deviate from them.
>
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>
> -Justin
>
> > ; Electrostatics
> > coulombtype     = PME           ;
> > pme_order       = 4             ;
> > fourierspacing  = 0.16          ;
> >
> > tcoupl                   = berendsen
> > tc-grps                  = System
> > tau_t                    = 1.0
> > ref_t                    = 300
> > ; Pressure coupling is on
> > pcoupl              = Berendsen     ; Pressure coupling on in NPT, also
> weak coupling
> > pcoupltype          = semiisotropic     ; uniform scaling of x-y-z box
> vectors
> > tau_p               = 2.0 2.0          ; time constant, in ps
> > ref_p               = 1.0 1.0          ; reference pressure (in bar)
> > compressibility     = 0 4.5e-5        ; isothermal compressibility,
> bar^-1
> > refcoord_scaling    = com
> > ; Periodic boundary conditions
> > pbc     = xyz                   ; 3-D PBC
> > ; Dispersion correction
> > DispCorr    = EnerPres          ; account for cut-off vdW scheme
> > ; Velocity generation
> > gen_vel     = yes               ; Velocity generation is on
> > gen_temp    = 300               ; temperature for velocity generation
> > gen_seed    = -1                ; random seed
> > ; COM motion removal
> > ; These options remove COM motion of the system
> > nstcomm         = 10
> > comm-mode       = Linear
> > comm-grps       = System
> >
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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